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statistics

FastqDeduplicationStatistics

Bases: BaseModel

Statistics for Fastq deduplication

Source code in capcruncher/api/statistics.py 
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class FastqDeduplicationStatistics(BaseModel):
    """Statistics for Fastq deduplication"""

    sample: str = "unknown_sample"
    total: int
    duplicates: int

    @computed_field
    @property
    def percentage(self) -> float:
        return self.duplicates / self.total * 100

    @computed_field
    @property
    def unique(self) -> int:
        return self.total - self.duplicates

FastqTrimmingStatistics

Bases: BaseModel

Statistics for Fastq trimming

Source code in capcruncher/api/statistics.py 
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class FastqTrimmingStatistics(BaseModel):
    """Statistics for Fastq trimming"""

    sample: str = "unknown_sample"
    read_number: Union[int, float]
    reads_input: int
    reads_output: int
    reads_with_adapter_identified: int

    @computed_field
    @property
    def percentage_trimmed(self) -> float:
        return self.reads_with_adapter_identified / self.reads_input * 100

    @computed_field
    @property
    def percentage_passing_quality_filter(self) -> float:
        return self.reads_output / self.reads_input * 100

    @classmethod
    def from_multiqc_entry(cls, entry: pd.Series) -> "FastqTrimmingStatistics":
        return cls(
            sample=entry["sample"],
            read_number=entry["read_number"],
            reads_input=entry["r_processed"],
            reads_output=entry["r_written"],
            reads_with_adapter_identified=entry["r_with_adapters"],
        )

    def __add__(self, other: "FastqTrimmingStatistics"):
        return FastqTrimmingStatistics(
            sample=self.sample,
            reads_input=self.reads_input + other.reads_input,
            reads_output=self.reads_output + other.reads_output,
            reads_with_adapter_identified=self.reads_with_adapter_identified
            + other.reads_with_adapter_identified,
        )